Class FlexibleAlignment

  • All Implemented Interfaces:
    Alignment, ARAlignment, EditableAlignment, UnequalLengthAlignment, SymbolList, Changeable

    public class FlexibleAlignment
    extends AbstractULAlignment
    implements ARAlignment, EditableAlignment

    FlexibleAlignment is a class which implements UnequalLengthAlignment, ARAlignment and EditableAlignment It places no restriction on where any sequence can be in the alignment so there could be gaps in the alignment. You tell it where to put the sequence, it will do it. I think I will be adding an Exception NonContinuousAlignmentException. STILL UNDER CONSTRUCTION. seqString does not work because there it does not seem to support tokenization 'token' this is true for SimpleAlignment too.

    David Waring, Matthew Pocock